Invasion of Equestria
by MLP TARDIS Adventures
Summary: Twilight has just had her coronation. After several days, she is already fed up with this. She finds a mysterious pony who later discovers is something that she thought never existed.
1. Stress and Mysteries

**UPDATE: Chapter has been fixed. Enjoy this story!**

It hasn't even been a week since Twilight's coronation and she is already stressed out with all of the "Congratulations, Twilight!" and "Good job!" All of Equestria has turned their attention to her. Most of her friends have probably not noticed her stress, but Fluttershy has. She has noticed this ever since the coronation. She asked what was going on during the party.

"You know Twilight, you looked nervous when you were giving the coronation speech."

Twilight looked over at Fluttershy.

"I don't know Fluttershy, I wasn't expecting to be a unicorn the first minute, then an alicorn the next. Also, almost everyone in Equestria knows my name now! Adding onto it the stress. What am I supposed to do? Am I now expected to handle nearly impossible tasks that only I can do? And what of my friends? Will they be abandoned, left alone with nopony to notice them ever again? I know I've handled hard things, but I don't want to deal with diplomatic relations with friendly and hostile nations!"

Fluttershy stopped her at that sentence, noticing a little crack in Twilight's voice. "Twilight, I don't want to interrupt, but I think you should only worry about this when the time comes."

Twilight took her advice. There's no need to worry about the future. That's something she learned quite a bit ago.

The party was even bigger by the time they got back to the castle. Pinkie Pie was bringing out the cake, Applejack selling apple pie, Rarity showing off her latest clothing, and Rainbow Dash... well, she was doing what she normally does at big Canterlot parties. At first she was drinking apple cider, then she went all woozy and probably past out on a table. The last ponies saw of her was her heading over to the Wonderbolts section. Typical Rainbow Dash.

There was no sign of Rainbow Dash after the party. She was found by the station unconscious about a day later. Nopony knows how she got there, not even herself! There was also some reports of an explosion about twenty miles from the castle around the time she was found. Some think that the two events are connected. Others think it was a coincidence. Which one does Twilight think? She's in the middle. She's not a conspiracy theorist, but neither is she one to dismiss something that happened conveniently at the same time Rainbow Dash was found.

**2 days later**

New day, new sky, new life. Somehow Twilight forgot about the coronation, so she was pretty happy while at the library. As soon as she walked outside though, all she heard was, "Congratulations, Twilight!" Ugh.

Walking through the crowd of who knows how many, she saw a face that she hadn't seen before. She wasn't able to get a good look at the pony. When she looked around for that pony again, so sign of him or her. Twilight was able to get into Sugarcube Corner without being torn to bits. She told Pinkie Pie about the mysterious face she saw walking over there. As usual she dramatically gasped and darted around everywhere preparing for a party.

The hard part was over, now she just needed to get quills. When she got to the Quills and Sofas store, they were out of quills. That is just impossible. The same old things were done for the rest of the day. She went to Applejack's to pick up some apples, helped out Rarity and Fluttershy. Watched Rainbow Dash do her tricks. Pinkie Pie didn't need any help, she was to busy sending out invitations.

Finally, nighttime. Two things to do tonight. One, be calm for a little while. Two, find that mysterious pony. She stayed calm for a while, waited for Spike to go to sleep. When he was asleep, she went to find this mystery pony that has been poking around everywhere.

Three hours and two just plain weird moments later Twilight finally found this pony. She could finally find out who this pony is. Twilight snuck up to him, it's definitely a stallion. The stallion probably knew she was there. When Twilight was almost next to him, she heard a quiet, calm, hello. Twilight responded back. "Hello, who are you?"

It seemed as if this pony did not want to turn around, or say his name.

"Hello? Who are you? Can you please turn around so I can talk to you?" He turned around slowly, revealing his calm, young face.

He was a dark grey color with extremely dark brown hair. His eyes were a dark green and he wore a black coat with a watch on it. His cutiemark was an almost empty hourglass. If you looked carefully at the cutiemark, you could see the sand grains dropping. "What is your name?"

He went quiet for a moment after, then he responded. "Does it really matter? My name is lost in the shadows and the depths of the deepest ravines. My name is hidden for the sake of the universe. If it is released, the universe will be on the brink of- Oh, sorry. Thought you were someone else."

When he said 'someone' she thought he was some sort of loon.

Twilight blocked that out for now because something about him wasn't right. It wasn't something that would be noticed by most ponies, but his eyes, they weren't right. They looked heavy and sad. They also looked old, very old. They looked as if they were done seeing the world as it is. She asked his age to try to find out who he is.

"If I can ask, how old are you?" He looked at Twilight with those heavy eyes carefully. He then responded with the last excuse she could hear.

"My age doesn't matter at all now does it?"

"All I want to know is your age, could you tell me?"

His eyes then got a little narrower when he told her that she wouldn't believe him. She then got upset that yet another excuse was given. Her voice sounded angry when she almost burst into flames (again) until he responded halfway into her sentence.

"Tell me your age! You have not answered since I walked over and I am-" His voice then over-talked hers as he said his age.

"1,208!" He was right, believing was not an option.

She looked at him as if he was an then the greatest enemy of a conversation arrived, a slamming door. She looked over at the slamming doors location, but there was no doors slamming. Twilight looked back to where this pony was, but he was already far down the road, running, and not stopping. There was no way to catch up, so she just walked back home. Nopony was outside, so it was very peaceful. She got back to the library to a nice clean room. This week has been an oddball of sorts, but the mysterious stallion is still itching her brain. Who is he? How old is he really? Hopefully her questions will be answered soon. For now, sleep is needed.


	2. The Attacks

**Hello everyone. As you probably know by now, this story will take a while to complete. But, I promise it will be filled with adventure, and even plot twists! Oh and also, minor updates have occurred.**

The sunlight came flooding through Twilight's window. Birds began tweeting a song, but Twilight lay sleeping like a rock. Spike was wide awake though, sorting out books misplaced on shelves. A little while later Applejack came in. "Hey Spike, Twilight up yet?"

"No, she's still sleeping."

"She must be tired after all that running around thi-"

At that point, a huge crash shook the whole town, literally shooting Twilight out of bed and into a bookcase. "What in the darn tootin' was that!"

Spike went to go help Twilight up. "Guh, Spike what was that? It probably shook the whole town!"

Applejack ran outside to see what had happened. "Uh Twi? I think that shook more than Ponyville."

Spike and Twilight ran outside and looked up towards Canterlot. The tallest tower of the Canterlot Castle was collapsing and falling down the deep cliff below. Ponies from Canterlot could be heard screaming from Ponyville.

A few miles away into the Everfree Forest, a dark grey colored pony was walking along a trail, only to stop suddenly at the doors of a police box. Then he heard the crash. He ran into The box suddenly and closed the doors behind him. The box then disappeared emitting a whooshing sound behind it.

**Meanwhile, in Canterlot...**

The princesses have been evacuated from the castle to Manehattan. Shining Armor and a battalion of Royal Guards have been brought to the castle to find out what had happened. Shining Armor was supposed to go back to the Crystal Empire today, but instead he's here helping out.

"Lieutenant, get five guards in to get ponies out of the castle. Two will stay with me, and the rest are to secure the perimeter. Nopony is to get in, don't even let the princesses in until we have done a full search of the castle."

Shining and the two other guards went in to find the source of the explosion. They didn't find much. Lots of debris and dirt. Then, they found it. They could barely see it due to all of the dust and dirt, but they could just see it. "Okay, quietly get over to him and arrest him."

The guards quietly ran over, but didn't come back. All that was heard was a laser and screams. The thing then slowly went over to Shining Armor. The thing talked with a screechy voice to Shining.

"Tell the residents of your world, the-" The thing paused. "Activating detonation sequence!" That was Shining's que to run.

"10, 9, 8, 7, 6..." The counting faded as he ran closer to the exit. Then, boom. Half of the castle went up in flames as the strange thing exploded. The CFD, MFD, and PFD were called in to stop the fires. About a mile away, a blue box appeared, and out stepped a dark grey colored pony.


	3. A Meeting

**Okay, before we begin, I just want to say wow. I wasn't thinking this would even get over 10 views in one month! It's only been 3 days, and I've already got readers from 8 countries! That's all, and enjoy this short chapter!**

**Two weeks after the Canterlot explosion**

Twilight decided it was time to tell her friends about the mysterious pony she found a couple weeks ago. She thought she shouldn't mention it to Pinkie Pie though. Pinkie was already upset that she did a lot of party planning for nothing, so she just gave a party to Gummy instead.

"So yer sayin' that this lunatic said he was 1,208? He must be more dumber than a snake givin' a mouse tea!" Applejack was probably right. This pony was acting crazy, but not a normal crazy.

"Fluttershy, what are you looking at?" said Rarity as she looked over at her. "What? Oh, nothing, just thinking."

"Bahahahah! He obviously was dumb! Nopony is older than the princesses! He must be from Crazetopolis!" You probably know this as Rainbow Dash.

"I know it sounds crazy, but something wasn't, well, right. His eyes, they looked old. Very old. He was also saddened to death, as if everypony he ever known has died in front of his face."

Rarity looked over at Fluttershy again, only to see her staring at the window. "Fluttershy, what is it? Is there somepony spying on us?" As before, Fluttershy said no.

Applejack decided that she should say something to Twilight she's wanted to since she first noticed all the stress hitting Twilight. "Y'know Twilight, I've noticed that you've been stressed out lately, wanna talk about that?"

Twilight only looked at Applejack. The then looked over at Fluttershy. Fluttershy was still standing in that same spot staring at the window. She went over to Fluttershy and tried to snap her out of the thinking.

"Fluttershy, you haven't said a thing since you got here. Something wrong?" Only this time, she didn't answer. She stared blankly at the window, just looking at it.

Then abruptly, Fluttershy came out of her trance. "We need to get out of here."

"Um, why darling? Is something wrong" Rarity looked worried when she said that.

"Something is coming. Something bad and dangerous. We need to get to Canterlot." Fluttershy said it with a scared voice, as if she had just met her worst nightmare.

Three knocks then hit the library door. One, two, a pause, then three. Everypony went silent. Then again, One, two, three.

Applejack was the first to say something. "So, is anypony gonna get that?"

"I'll get it!" shouted Pinkie Pie. She looked out the door, nothing. She closed the door and got back into the conversation. Behind Rarity, an odd whooshing sound started. They all looked back, only to find a blue box appear. Out stepped a dark grey pony. "Oh hello, hope I'm not interrupting."

The friends only looked at each other. Pinkie Stayed silent, then looked at the dark grey pony, then at the box."Question is, how did HE get here?"


	4. Surprise

**Sorry that I haven't been making new chapters lately, I've been busy with this one, starring the CMC! Also, people from 12 countries have viewed this story! Well, let us begin! Geronimo!**

Everypony in the room was silent, dead silent. The mysterious pony was looking around as if he's never seen them before, which is true. He hasn't ever seen any of them, that he thinks.

"Um, am I interrupting anything?"

Twilight looked into his eyes just to make sure it was really him. "Actually no, you're not. You're needed here."

The mysterious pony looked confused. "Uh, you do? I don't recall us ever meeting really."

Twilight was completely surprised. She thought he would remember an odd first meeting, which happened to be several weeks ago.

"Are you crazy? You DON'T remember several weeks ago? I'm starting to think you are nuts!"

Rainbow Dash came in by asking him, with a stern voice, what his name was. "Yeah, and what is your name? Everypony here has been trying to find what your name is. Now that you're here, tell us!"

As before, the pony was confused, he asked them something, but quietly. "If you lot could just calm down, I'll answer all of your questions."

"Then what is your name" said Rainbow Dash talking calm, but still stern.

"I'm The Doctor."

Applejack heard all she wanted to hear. He's not going to tell them his name. "Doctor ain't a name, it's a title. How 'bout telling us yer real name?"

Rarity wasn't out to find his name, she was crazy to find out how he got that accent. "Where did you get that exquisite accent? It's so remarkable!"

Then everypony, accept The Doctor, began shouting, talking, and Fluttershy trying to get everypony calm. The Doctor has had enough, he's already gathered too much attention. He had to get out of here. He found the right moment and ran out the library door. Nopony saw him run. It was about 5 minutes until Applejack noticed The Doctor was gone. "Hey! Where'd that lunatic doc go?"

They all looked at the entrance. The door was wide open. On the doormat though, was a strange device. Applejack went over to it and picked it up. "What in darn tootin' is this silly doohickey?"

Rarity snatched it out of her hooves and examined it. "It looks like, well I don't know!"

Twilight was able to see the strange device. "It looks like an artificial horn, meant to," she looked at it and found the button, she pressed it. "It's for opening doors..."

Pinkie gasped when she heard that. "Maybe that doctor pony can't open doors! So he has a special tool do it for him!"

Everypony looked at her. Most likely not the answer. But there's always a possibility, saying that Pinkie is usually right.

Twilight looked at it closer. "Hmm, no it's more than just opening doors. It looks like-"

"Maybe it's a laser weapon that can annihilate entire universes and was made on the planet 'Pablo 7'!"

That was it. Twilight was now determined to find out who he was, no matter what the cost. The strange box that he came in was still there. It may be small, but she was going to go in and find out who he was. "Alright girls, we need to find out who he is. He's been poking around a lot, especially around the library. We'll start by looking inside that box there."

Twilight wasn't going to wait to get an answer from them, she was going to go in there. She went up to it, and pushed open the doors. She walked inside, only to back up slowly out of it. "It's, but, that's, that's impossible!"

**A couple miles away**

The Doctor stopped running at a tree fort. He was tired from running that fast. "Wow, it's amazing how fast ponies can run. I probably ran about a couple miles in minutes!"

"Hello? who's there?" Three heads popped out of the tree house window.

"Oh, hello, am I interrupting anything? No, no. That was an awful sentence, I already said that..." The Doctor was now arguing against himself, which seemed weird to him, but at the same time fine.

"Uh sir, are you okay? You aren't hurt or anything?"

"Oh, no I'm fine. Just blabbering to myself. Oh, hello, I'm The Doctor. You three are?"

The trio all said their names in order, from left to right. "Ah'm Applebloom." I'm Sweetie belle." "And I'm Scootaloo!"

The Doctor was thinking about how interesting the names are on this planet, but then he remembered it's very late. "Say, why are you three up this late?"

Scootaloo told him why. "I found something over by Sweetie belle's house, we were just about to go and see it."

Now The Doctor was excited. He didn't care whether or not the thing was boring, he just needed something to do. "Hm, can I come along?"

"Okay! It's very cool!" Scootaloo was very excited to show not only her friends, but a grown-up as well.

They all walked down near Sweetie belle's house where Scootaloo found whatever it was. "Here it is, isn't it cool?"

They all looked down at it. Applebloom and Sweetie belle were amazed, but The Doctor only looked down at it. "That shouldn't be here. Unless, hmm."

The Doctor picked up the said with a calm voice; "I'm going to have to take this for a check. Take one last look at it."

The trio took one last look at it, and then The Doctor walked down the road and took a sharp turn. The CMC merely waited for him where they were.


	5. Preparation

**15 countries have now seen this story! What a good story I'm guessing this is coming out to be! You might want to get ready, a familiar pony is coming to blow you all off of your chairs! Prepare the hate shelters!**

Twilight and her friends boarded the train to Canterlot. They will be the fist civilians into the city ever since the castle blew up. The new temporary capital, Manehattan, has been preparing for another explosion, since everypony has been following this for the past two weeks. On the mini T.V. set that was in their car was set onto the EBC, Eagleland Broadcasting Corporation, and was covering recent discoveries on what probably happened in Canterlot.

"A new discovery from last night probably changed the tides on the theories of the Equestrian capital Canterlot explosion. We now go live to Canterlot to talk to Flash Sentry, a royal guard who saw the pony who possibly caused this explosion."

Twilight was glued to the screen while he was talking. This was probably the fist time she could see him without having to look away every couple seconds.

With the other five were busy with something else and Twilight not paying attention to what he was saying, they missed a key clue to what happened. But Twilight snapped out of the trance just in time to hear two words she wanted to hear. "...blue box..."

Twilight jumped out of her seat into the next, where Rarity was sitting thinking about that accent. "Rarity! Did you hear what he said? He said-"

A voice from the back cut her off. "You mean your crush?"

Twilight looked to the back and saw Rainbow Dash laughing, and Applejack in the seat in front of her trying not to laugh. Twilight only responded with a flat "no" and went back to talking to Rarity. "Anyways, he said-"

Applejack interrupted her and said with an attempt to make a little deeper voice "I love you, Twilight."

Twilight darted out of the seat and into the walkway to see Applejack and Rainbow Dash laughing their rumps off. Pinkie Pie was giggling in the seat across from where Rarity was sitting, and Fluttershy was merely doing nothing. Twilight gave Rainbow Dash and Applejack the creepiest stare. Applejack and Rainbow Dash's laughing quickly faded off and said "We'll stop talking now."

Twilight now was able to say what she wanted to say. "He said blue box. That probably means that the pony we saw last night was the pony who caused the explosion!"

"That pony? He didn't seem that harmful to me." Fluttershy said with the loudest quiet voice she's used in a while.

"He was actin' a bit too strange last night." Applejack now was acting serious. They were talking about the possible pony who caused devastation to Equestria.

"We'll just have to find out when we get there. And no more Flash Sentry talk at me. I do NOT have a crush on him!"

Applejack seized the moment yet again. "Oh yeah? Say that to when you was starin' at them there screen when he was on it!"

Applejack and Rainbow Dash burst into laughter, Twilight said nothing and sat back down in her seat.

**Meanwhile in Manehattan**

The princesses were at the Empire State Building Observation Deck looking out at the beautiful city below. A filly was standing behind them looking up to where he thinks there heads are. Luna turned around, smiled, and looked back at the city. The filly got a little frightened, and ran back to his parents. Celestia looked over, and also smiled.

"You know, Celestia, this explosion of some sort that happened, there must be something behind it. None of our loyal ponies would do this, and we have nothing but good relations with every other country. Who would possibly want to break relations with a strong country such as ours?

"Luna, I have a felling that nopony on this planet would do such a thing, and that the explosion was caused by something else. If we could find out what that something else is, we could get to the bottom of this and go back to Canterlot."

"Sister, do you think it is necessary to send Twilight and her friends to Canterlot to try to find out what happened? We have every expert and crime investigator we can get at Canterlot!"

"Luna, if we could go to Canterlot and settle this, we would. But the Royal Guards won't let us due to fear that we are being targeted. Twilight and her friends also are very good at finding things that are out of place. Let's just hope that this will be the end of this nonsense."

"I hope you are right, sister." Luna and Celestia looked back at the city.

**Meanwhile in Ponyville**

The Cutie Mark Crusaders were following The Doctor. They were talking with him about all kinds of stuff. "So this picture on my rump is a 'Pruney mark'?"

"Uh, no, that's a cutie mark."

"Ah okay, 'cootie mark', got it."

"No, a CUTIE mark!"

"Oh a cutie mark! Okay!" The Doctor was having trouble blending in with the locals. He had no idea this world even existed! This was all brand new to him, other than grape jelly, which he had with him at the time.

"So mister-"

"No, it's The Doctor."

"Oh okay, Doctor, what was that thing I showed us last night? Why did you take it to your blue house?"

"Some things are meant to be kept a secret. Now, if I may ask, why don't you three have 'clutie marks'?"

"It's cutie marks, and we haven't found ours yet. We still have a chance at finding our talent."

"Oh! Very interesting! This is fun! New everything here, besides grape jelly!"

"Say, what is your talent Doctor?"

"Well, judging from my 'cootsey mark', it must be, hmm, an hourglass, hmm..."

"It's cutie mark, and your talent must be time!"

The CMC's gasped all at once. "Are you a time traveler?"

The Doctor looked at them. "Well aren't you three clever! Yes I am a time traveler! Oh, and shush, don't tell anyone."

"Don't you mean 'anypony'?"

"Anypony?" The Doctor burst out in laughter and couldn't stop laughing. "Hahah! Anypony! That is funny!"

"You sure you're okay mister? You're acting strange."

Ha, don't worry. Time travel can get me into all kinds of situations."

**Meanwhile under Canterlot**

"Is the warp ready"

"Yes. Prepare countdown warp to Manehattan. Set countdown, 500 rels."

"I obey."

"Send message to flagship, invasion ready in 500 rels."

"499, 498, 497, 496..."


	6. The Past Comes Back

**You see what I did in the last chapter? EBC, BBC? No? Okay, well we're going to see some plot twists! Huzzah!**

The six friends looked out of the left side of the train car. Canterlot lies in ruins because the fire spread to other buildings. The train was forced to stop before the station. Three ponies got on the car the friends were on.

"Hello, I'm Colonel Fredrickson of UNIT. We are required to stay with you while you are here. Civilians are not allowed onto the premises, and we fear that all alicorns are being targeted."

The train continued up the tracks to the station.

"You see, we do not know what caused the explosion, but UNIT has dealt with similar cases before. We believe it was an external force trying to get in, with hostile intents."

"So yer' sayin' that aliens had something to do with this? That is nonsense!"

"Yes, it sounds non-sensible, but only a select few know what caused this. I am not one of them."

Twilight was curious of who they were. "Who are the ones that know who did this?"

The corporal that was there then spoke. "Only UNIT personnel may know who. You six are-"

"Corporal Henry! I do believe you were told to read article 3 of UNIT rules."

"Oh yes, sorry sir."

"What is article 3? Also, who knows what caused this?"

"Article 3 is a set of rules created by Brigadier Lethbridge-Stewart that requires all ponies helping UNIT to have every question answered. Article 3 is very complex, so I can't show you it nor tell you the rules within it."

"Okay you've answered that, who are the ponies who know who caused this?"

"Only three know who caused it, one of them is dead though. Brigadier Lethbridge-Stewart, Sarah-Jane Smith, the deceased one, and The Doctor.

"The Doctor? That's the pony we saw in ponyville!"

"You've met The Doctor? Corporal, sent a message to The Brigadier that we have found six associates to The Doctor.

The colonel then turned back at the six.

"You three are now bound to know something only a hoof-full of ponies know. Not even the princesses themselves know about this."

The train stopped at the station. Everypony got off and looked that the burnt city. A pile of bodies were in front of a building that was still standing and nurses taking care of those that were still alive. Fluttershy felt as if she was in a nightmare, or worse.

Three guards were standing in front of a large door that looked as if it led underground. The Colonel motioned everypony towards the door. The guards opened the door for them. The door was possibly extremely heavy while Twilight watched them open it.

"Alright, I'm going to warn you all before we go down. There is highly toxic things and dangerous weapons down here, so don't touch a thing."

They all continued down the long winding stairs. It let to the catacombs below the castle where Twilight was trapped during Cadence's wedding.

"The Royal Guards found this a long time ago, around the 1500's. Everypony knew about it until the 1740's when Britain invaded most of the country. In order to prevent a surprise attack when we took the city back, every file about the catacombs was burned and destroyed. The princesses have long forgot about it, but some remembered. Another society called Torchwood came in possession of a file on the catacombs. They held onto it until around the 1970's when they sent it to us. We set up a base down here and have been here ever since. From what we know only 13% of the catacombs have been discovered."

All around them was machinery, drilling, charts, maps, x-rays, and lots of other stuff.

"So why are you showin' us all of these contraptions and doohickeys?"

"You are associates to The Doctor, and according to article 1, we are required to show anypony, or anyone, to all that is needed for them to help The Doctor."

"Okay, then what is it you need to show us?" Twilight was nearly drowning in her thoughts.

"This is a chart of the sound waves under the catacombs over the past month. As you can see, starting two weeks ago, the same day the explosion occurred, the sound wave chart has risen from 8% to 82%."

"Is that really it? That ain't a thing that hints that aliens have a say in this!"

"This is only the start. We began an investigation three days before the other investigators came and looked around. We found this." The colonel lifted up a strange type of laser.

"Haha! It looks like a skewer attached to a bunch of other bent skewers!" Pinkie Pie could barely stand while laughing, and the colonel only stared down at her as if she was an alien. He was thinking she probably was.

"Also, we found a half burnt security tape of the room that contained the first explosion."

The Colonel put the remains of the video tape in the projector. On the screen there wasn't a whole lot to see. There was lots of smoke. The smoke began to clear, and what was there was what looked like a bent cylinder, half spheres sticking out of it, and a dome on the top of it.

"Ahahaha! That thing looks so stupid! Whats that thing on the side of it? A toilet plunger? Hahaha!" Rainbow was laughing so hard she was crying. She was almost choking on her laughing.

The tape continued, then stopped. Twilight thought she saw something at the end of the tape. "Colonel, can you rewind the tape two seconds before the end, and play it one frame at a time?"

The colonel did this. The film was going by extremely slowly. At the last three frames, there was a shadow of a pony in a running position going from the left to the right in two in a half frames. "When the expert went over this, they didn't see that. Corporal Henry, bring the last three frames to the visual experts and the census scanner. We need to find out who this is."

The last frame played one more time. The spot where the eye might be was dark green, though the green could barely be seen. Although the film stopped, the eye followed Twilight down the hall until she went out of sight, then the eye went back into place.


	7. The Demon Awakens

**Okay, so those who watched the New Who season 4 finale, you (probably) know who the pony was in the film. If not, on we go! Oh also, Torchwood, UNIT, what else will I put in? Spoilers ;)**

"So let me get this strait" Scootaloo was having trouble taking in The Doctors words, so she is trying to guess what he's saying. "That thing I showed you the other day is alien?"

"Yes, although I thought it was something else. I thought it was, well, never mind."

"Anyways, can you show us the time machine you have?"

The Doctor turned around and looked at them. They had the 'pweeeese' eyes on, one thing he couldn't say no to. "Well okay. But you can't touch a thing okay? Time machines can be very, very, dangerous if not used properly."

"Okay!"

They all walked over to a blue box sitting in a dark alley. The Doctor pulled a key out of a tiny pocket on his bow tie. He also pulled out his sonic screwdriver from the pocket too.

"Aaaaand, voila! Welcome aboard the TARDIS!"

The three fillies all looked like they ate an extremely sour pickle. Was this tiny thing really a time machine? "Uh, Doctor? This is tiny, how is it possibly a time machine?"

As usual The Doctor had to urge them to go in. "Oh, you'll be surprised. Go on in."

The CMC's all slowly walked in as The Doctor smiled as he watched them go in. They slowly backed up with their mouths wide open. "Well what did I say? You lot would be surprised!"

"But, bu-but, that's just impossible!"

"Ha, well not where I come from! Come on, let's go to..." The Doctor then paused. "Where would you three like to go?"

"We don't know! How about something adventurous and fun!"

And grand-slam! The Doctor now understood their language loud and clear! "Alrighty! Come on, let's go!"

They all ran into the TARDIS. The TARDIS wheezed and whooshed, disappearing from sight.

"Right, so, welcome aboard the TARDIS. Details will be given along the way, our first stop will be-" A loud boom and crash interupted him, followed by the cloister bell and a red light. "No, no, no! Don't start now! No!"

"Whuh, whut's happenin'!"

"Well, it seems UNIT, or Torchwood, has found me, and they are towing us in. The TARDIS is trying to fight back because the override code wasn't sent to me. No matter, I'll just put in the override myself!"

The Doctor pressed a bunch of buttons and pulled levers, and the room settled back to its original state before he was interrupted. "Right change of plan. UNIT, or Torchwood, is towing us to them. We'll have to help them with whatever they want, and then we will get back on schedule!"

**Meanwhile in UNIT Canterlot catacombs base**

"Sir, we've found the TARDIS. We are bringing it in now. The Doctor gave us the override code."

"Oh good! Tell the brigadier that he The Doctor has arrived."

"So, uh, who is this Doctor? Is he a medicine type of doc?"

Pinkie laughed. "Maybe he's a cheese doctor!"

The colonel looked at Pinkie again. "How absurd." he thought. "I think all of your questions will be answered when he arrives."

The TARDIS then began appearing next to the colonel and was whooshing and groaning steadily. It then stopped, and a deep, loud, thud, indicated it landed. Twilight and the rest of her friends went over to the blue box. Out stepped The Doctor and the three fillies. "Oh hello! By the looks of the hats, this is UNIT?"

"Scootaloo? Applebloom! Sweetiebelle!? How are you three here!"

"Oh, you three- wait one moment..."

The Doctor walked slowly five steppes, and stopped. "Something is here. Something that shouldn't be here. Something dangerous and bad."

"Doctor? We assure you that the base is secure. Check th-"

"No no. It was let in." He sniffed the air. "Is there a security tape anywhere?"

"How did you know? Have you already experienced this Doctor?"

"No, but I want to see the tape. Show me it."

They all went over to the tape. The Colonel then played it, and The Doctor watched.

"Daleks..."

Rainbow Dash shot up. "What did you say that thing was?"

"It's called a Dalek."

Rainbow Dash then lost it. This was all too funny, and she let out a laugh that probably lasted a century.

Then the last frames played. "Play the last three frames again." The final three frames played slowly, then stopped at the last frame. "Colonel, burn the tape..."

"What did you just say?"

"Burn the tape! You let it in! Burn it! Now!"

"Yes sir!"

Too late though. The room began to get darker and darker, even though all the lights were on. The ponies picture in the last frame begins to disappear. The ponies picture then disappeared and the darkness disappeared as well.

"What in celestia was that?"

Rainbow Dash wasn't laughing, she was frantically looking around, trying to find what that was.

"Colonel, you made the biggest mistake in the history of this planet."

"But sir? What did I do?"

Rainbow Dash was staring into a corner, with a tear beginning to form. Fluttershy looked over at her. "Oh my, Rainbow Dash what's wrong?"

Rainbow Dash only lifted her hoof and pointed at the corner. Everypony in the room looked to that corner and saw a blue pony with blonde hair, staring at the ground, and was covered in blood. He was chuckling softly at the ground. As he looked up, his laugh got louder. He was looking up completely, and staring at The Doctor. His face was cut and had blood running down it. Everypony in the room was cowering, aiming guns at him, or just staring. Scootaloo looke at Rainbow Dash. She had never seen Rainbow Dash this scared before.

"Ahahahaha... hello again, Doctor."

The Doctor was mortified. "But, you died. I watched you die. How are you alive?"

"Save it for later Doctor. I have an invasion to start up." The mysterious pony then started punching the ground. Every punch made a deep dent into the ground, until he stopped suddenly.

In the hole, a countdown was coming to the last ten seconds. The Doctor knew what the voices were. Daleks.

"Five, four, three, two, one! Begin warp to Manehattan!"

Beams began shooting up and over to the UNIT catacombs doorway. The pony then yelled; "Welcome to the new era, Doctor! The Dalek era!"

Beams were shooting out towards Manehattan. UNIT soldiers were firing at the beams trying to at least slow them down. The Doctor only stood there in horror, staring at a 3-D painting.

"No, it can't be. No, no..."

"Doctor, who is he? What are those? What are they doing!"

"It's an invasion. A Dalek invasion. And..." The Doctor took a deep breath. "An invasion leaded my one of my greatest enemies. The Master."


	8. Declaration of War

**Enjoying? Good. Expect for each chapter to get to the big chapter, the chapters number I am not sure yet :P. Well anyways, allons-y!**

Space, the final frontier. These are the voyages of the starship _Enterprise_. Its five-year mission: to ex-

"Uhm," The Doctor was looking up at the ceiling. "I think you have the wrong story up there."

Whoops, sorry.

Laser-like bullets were flying out of the hole that The Master punched out. The colonel gave the order to fire at these lasers. The room was filled with gunfire and laser shots. Everypony's ears was in pain because of this. Over all the gunfire and the noise, The Doctor yelled to everypony one simple order. "Out! Everypony get out of here!"

Everypony stopped firing and trying to get into cover and ran to the entrance. The door was jammed. "Great, it's a deadlocked door. Anypony have a code to unlock it? The sonic screwdriver can't- wait. Where's my sonic screwdriver?"

Twilight remembered the weird object she put on a table at the library. She decided not to say anything about it."So we're trapped in here?"

"I'm afraid so. Without the code or sonic screwdriver-"

Scootaloo tugged on his bow tie. "We could always use your police box thing."

"No, this is a UNIT base. They make secret bases TARDIS-proof. Even with the TARDIS in, we can't get out. Only the brigadier knows the code to make a room unTARDIS-proof."

"Wait," Twilight was getting in position to do a spell. "I know a teleportation spell that can get us all out of here." The room began to glow a light purple, then they all teleported from the room to Manehattan, in front of the Empire State Building to be exact.

Twilight was extremely dizzy. Teleportation spells take a lot of magic. Teleporting about 50 ponies takes a ton of magic. A crowd had gathered around the 50 teleported ponies. The Doctor decided to "shoo" them. "Don't worry! Nothing to see here, go back to your shopping and sight-seeing!"

Rainbow Dash looked up at the top of the building. There was brownish-red lasers going into it. "Uh, Twilight? Aren't those the weird laser things we saw in the base?"

"It looks like it."

"Right, we have to get up there and find out whats going on. Any volunteers?"

"UNIT always follows orders, sir."

"Don't call me sir."

"Sorry."

"Okay, how about you 6? We may need your- well, we NEED your help."

Stares were traded among them for 10 seconds. Twilight then said yes, and they all went inside, and up the stairs.

**Meanwhile on the Observation Deck**

"Prepare teleportation!"

"I obey."

"Sister, what are these... these... things, doing?"

"I don't know."

"You will stay silent, or you will be exterminated!"

The door flung wide open. The Doctor in the front, gasping for air, said something first before anypony. "Whew, over- over 100 flights- flights of- stairs..."

"It is The Doctor! Exterminate him!"

"Wait wait wait wait!"

The Daleks didn't move. They only kept their eyestalks staring at him as if they were going to melt him. "Right, now I've got your attention, wait."

"Daleks do not follow Time Lord orders! You will be exterminated!"

"Fire!" The colonel gave the order to fire guns at the Daleks. They know the bullets won't hit them, they are just setting a distraction.

"Run!" Everypony in the group ran back downstairs besides The Doctor, who was trying to unlock the little cage Luna and Celestia were put into. "Right, get downstairs!"

**Meanwhile, further under Canterlot**

"3, 2, 1. Prepare warp!"

"We obey!"

A machine from before the renegade-Imperial Dalek war was activated. Because it was old, it took a long time to power up. In fact, the whole time it's been charging, getting ready to teleport hundreds of Mark II Daleks that have seen deadly combat.

"Teleporter charged! All Daleks board the teleporter!"

50 Daleks got on the teleporter. A light green pulse of light surrounded them, then they disappeared. More Daleks boarded the teleporter, and the same thing happened to them. On a little screen, writing that only Daleks can read was on it. If it was in English, it would say; "Destined target: Manehattan".

**Meanwhile, in Manehattan**

Meanwhile, in the Hall of Jus-

"Wrong story!"

Sorry sorry! Jeesh.

The Doctor was pacing back and forth. He was thinking. Not just about a random thing, but about how they got here, how the Daleks got here.

"So uh, who are you?" Twilight itched for the answer now.

"Well, I can't hide now, I already have been found." The Doctor took a deep breath in. "I'm The Doctor. I know here that you all have fancy names, but here, I am merly called 'The Doctor'."

"Now that don't answer much."

"Yes I know, A lot of questions probably won't be answered until later, much later to be exact. Anyways, I recommend that we find a place to stay. Say, aren't you 2 staying at the governors mansion?"

Celestia and Luna nodded.

"Ah good! We could stay there!"

Twilight felt like something was going to happen, very soon. If she could find that out, she could stop worrying, but no. Something is happening, something even bigger than the situation at the moment, but what was it?


	9. Finding a Piece of the Puzzle

**Happy 1,000 views! I've fixed up spelling errors in chapter 8, and I plan on fixing up the first chapter soon. Sorry about the story being slow moving, I've been planning out the end. Trying to look for the right time to add a Lyra moment.**

"Oh wow." Scootaloo looked up at the great big mansion that the princesses were staying in. Never before did she think she would meet them.

The great big group of ponies walked to the stairway of the governors mansion.

"Alright, UNIT members get to the UNIT base that's on 18th street." the Colonel demanded with a stern (and somewhat nervous) tone.

As all the UNIT personnel went to the base, the Doctor, Luna and Celestia, Twilight and her friends went up into the mansion.

"Right so, Daleks, bad news. By the looks of it they were running at a 69% efficiency, so their weapons must be offline. We have to get the building guarded so they can't get out. At the moment they may not be dangerous." the Doctor announced to the group of ponies.

"If I may, who are you? We tend not to receive orders from civilians, it gives us an awful reputation to the middle east." Celestia stated.

"Ah, right, yes, shall we just go in? I need to find a certain book that might contain something I need to stop the Daleks."

They all went in and went down the hall into the library. Books were stacked high, all in alphabetical order. The Doctor went looking for N.

"N, n, n, aha! Now, machinery that begins with n, here!"

The Doctor opened the book to where he thinks would be the piece of machinery would be.

"No, no, nope, no, wait... this world has nano-genes? How did you all find nano-genes?"

Celestia looked over and told him; "Starswirl the Bearded found them when he got a paper cut. Do you believe that?"

The Doctor's eyes got wide."Actually I do believe that."

The Doctor continued scanning through the book. "Aha! Neuron capacitator!"

He looked further down. He saw that they are located within the U.N. laboratory. The Doctor quickly got up, ran down the hall, and outside. The others quickly followed him. When the rest caught up to the Doctor, he stood still. His face was turning a light green. He looked over to his left, saw a trash can, ran to it, and puked inside of it. The group then was disgusted and turned around. The Doctor finally finished throwing up.

"Whew, got up a bit too fast."

He then started to the U.N. headquarters. The rest followed.

**Meanwhile, somewhere within the Canterlot Catacombs**

"Daleks have teleported to Manehattan. They will be completely teleported within the hour."

"Good. Tell me, is there news of, him?"

"No. He is unaware of our plans. Dalek Mark III's have been spotted in manehattan. What shall the others do when they get there?"

"Tell them to exterminate all of them. There can only be one type of dalek. That type of dalek will be..."

**UNIT base, Manehattan**

Many alarms were going off. A pre-recorded message was blaring through the building.

"WARNING! WARNING! UNIDENTIFIED TELEPORTATION INTERCEPTED! PREPARE CROSS-LINK!"

"Sir, sir!" A corporal was running towards the Brigadier.

"Yes? What is it?"

"We've identified the type of life form. It's dalek."

"Oh no."

"Sir, it's a different type. This one that hasn't been cataloged since the 1980's."

"Have you gotten an image of it?"

"Yes, here it is."

The Brigader stared down at the picture. "No, that isn't possible. They're all dead."

**U.N. Headquarters, Manehattan**

"Right, here we are! Drew a crowd, played a game of ping pong, invented the trilaphone, and now we're at the foot of U.N!"

They went up the stairs, got a special clearance by the guards, and went in to find the laboratory. The guards outside the laboratory gave them another special clearance.

"Hello, hello, hello! We are here for a Neuron capacitator!" The Doctor shouted to the scientists pretending they're busy.

"Oh, uhm, well, what for?"

"Have you not looked at the Empire State Building?"

"Oh, right, here."

The scientists gave the Doctor the capacitator. "Wow, it's really that easy? Don't you think that-"

"You are with 3 out of the 4 princesses of equestria. Even with 1 princess you have an ultimate clearance."

"Oh really?" The Doctor turned around. "Oh! When did you all get here?"

Twilight looked around. "Uh, we've been with you since the Empire State Building."

"Oh! Okay then!"

One of the scientists turned around at a lever. He looked at what the button next to it said. He looked back at the Doctor then.

"Right, We'll be off now!" The Doctor turned around again. "Oh hello! Who are you all?"

"Ugh."


	10. It's More Than What We Think

**Does the Doctor have amnesia? Maybe, but that isn't what we are focusing on at the moment. What we should focus on, is what type of Dalek is here. Oh, and this is the tenth chapter! Huzzah! Also, this version of 11th is a mix between 10th and 11th.**

The group of 10 walked down the stairway and onto the sidewalk. The colonel's walkie talkie began to receive static. He answered it.

"Hello? Oh, yes sir!" He looked over at the Doctor. "Oh Doctor, it's the Brigadier."

"Ah, the Brigadier! I'll take the walkie!" He put the walkie talkie up to his ear. "Hello, Brigadier! Any news that we need?"

"Yes, a teleportation activation has caused a big stir at the headquarters."

"A teleportation? By who?"

"The Daleks."

The Doctor had a grimace on his face. "I know about that already. There's a bunch of Mark III's in the Empire State Building."

"This is a different one, Doctor."

"What do you mean? They got rid of the Mark I's and Mark II's."

The Brigadier got nervous. "Doctor, they're Mark II's. But you'll never guess what type of Mark II's."

The Doctor got interested and stopped walking. The entire group stopped as well and waited for the Doctor. "Well? What kind of Mark II's?"

"Doctor, they're Imperial Mark II's."

The Doctor's mouth opened in astonishment. His pupils got tiny while he processed that in his brain.

"Oh no. That means..." The Doctor looked at the group he was with, and also made sure the Brigadier could hear. "Davros is still alive."

"What's a 'Davross'?" Twilight said while trying to listen to the walkie talkie.

"It's Davros. The creator of the Daleks. If he's alive, that means there's more to just the III's attacking and the Mark II's."

The Doctor quickly turned towards Ponyville, only to find an Imperial Dalek right there. It said to the Doctor in a gurgly voice; "Halt! You will come with me, Doctor!"

"Oh, alright. Okay, okay. Where to?"

"You will be taken to the Crucible II!" The Dalek turned around and faced another Imperial Dalek. "Exterminate the inferior life forms accompanying the Doctor."

"No, we have received orders to converge onto the tallest building of the city! Mark III Daleks have been reported there!"

"Fine. All Imperial Daleks are to converge onto the center of the city!"

More and more began appearing. The Doctor was being led down the road into a screaming crowd. 12 Daleks surrounded the 9 remaining ponies. (If you guys are wondering, the CMC are still at the mansion.) "You 9 will be kept hostage in a magic-proof cage!"

A cage appeared around them. They all heard what the Daleks said, so the alicorns and unicorns didn't you their magic. Rainbow Dash tried shouting at the Daleks, but they didn't listen. The cage started floating up into the air and into space, onto the Crucible II. They were put into the jail area.

**Meanwhile on the bridge of the Crucible II**

"The Doctor has been captured! He is being taken aboard the Crucible II!"

"Good, very good." Davros turned around towards a wall. "What do you say we do with him, Dalek Caan?"

Laughter came from where Davros was facing. "Ahahaha, I say, we use power to throw him back into the Time War and watch him collapse under the pressure of it! Ahahahaha!"

"Hmmm, good say Dalek Caan. Although we will need him to take over this world. We need to find his TARDIS as well. Get a search party to find the TARDIS at once. Kill anything that gets in the way."

Dalek Caan said to Davros again with his maniac laughter "But Davros, we both have seen what he can do. We must throw him in before he does anything to stop us."

"Yes, you are right. We will gather his companions to watch him die. Our new Dalek planet will soon be ours!"

"Ahahah, wait, I am picking up something." Dalek Caan went silent. "I am picking up a life form that is not pony on the planet. It is Cybermen!"

"No, no! How!? They must be stopped! TELL ALL DALEKS, FIND ALL CYBERMEN, AND EXTEEERMINATE THEM!" As you can see, Davros went into overload.

**News stations everywhere that speaks ****English**

"This is an EBC important news broadcast. Equestria has been attacked by an unknown species. All residents are to stay indoors until the Equestrian and Crystal army can settle what is going on."

"Species are being sighted killing ponies. At the moment, the life forms have been identified. All residents are to stay indoors until the situation is settled by the Equestrian Army and the Crystal Army."

Mmm, this is a good hamburger. Oh, whoa, that's it? I thought there was more stations than that! Oh, looks like I'll finish this burger later.

Anyways...

**Somewhere outside the universe**

"The target has been breached, sir."

"By who?"

"Daleks, and we think Cybermen."

"Oh, great."

"Although, we do have a Time Lord there, guess who it is?"

"The Doctor!"

"At least there's a chance. We will rise again, just wait and see."


	11. Story postponed

This story production has been postponed to September 1st, 2014. In the meantime, a new story will be created.


End file.
